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2006 Odyssey intake manifold runner control

In doing a timming belt replacement job at 105K on our 2006 Honda odyssey I disconnected the electrical end ( stepping motor? ) from the intake manifold manifold runner control valve to give extra clearance to move the steering pump out of the way. The stepping motor has a gear type connection between it and the actual valve in the manifold.
Question: Is there a timming procedure to use in reinstalling the stepping motor gear into the valve gear? Currently the stepping motor seems to be at a “park position” when removed and the valve gear is fully seated in the counterclockwise position while facing the valve gear. The van runs very smooth at all rpms but feels slightly sluggish and gas mileage seems to be also slighty worse then before. I suspect the IMRC is out of sync and possibly causing these suspected issues.
I went to a local auto repair that has a reputation for doing good work and asked the service writer about this. He said the engine would run poorly if out of sync and that when they get into this situation the car would have to go back to Honda to be set up correctly. Of course this is a option but I feel with the correct procedure I should be able to do this.
Timming belt, water pump, tensioner, both pulleys and exact same NGK plugs were all installed at this time. Presently there is about 3000 miles on this service and all seems to be good with the exception of the IMRC question.
Any comments would be appreciated.
Thanks !